Compound Heterozygote Filtering Rules.

<p>If both parents of the index patient are unaffected it is not possible that one of the heterozygous disease causing mutations is present in a heterozygous state in both parents unless a recombination occurred between this variant and the second compound heterozygous mutation.</p

Illustration of mapping artifacts resulting in false positive variant detection.

<p>The illustrated sample carries a mutation in the maternal copy of a pseudogene of <i>NBPF10</i>. If the pseudogene is not included in the reference sequence, the reads originating from this pseudogene are mismapped. This may result in a false variant call. Indicative for false genotype calls are proportions of reads supporting the alternate allele that strongly deviate from 0.5 or 1.</p

Exomes of 85 European individuals (CEU) as well as 88 African individuals (YRI) were filtered for rare compound heterozygous candidate variants.

<p>A) In average around 230 variants pass the filter in CEU exomes and 309 in YRI exomes. B) The potential compound heterozygotes are distributed over 31 genes in CEU individuals and 67 genes in YRI individuals. C) Altogether 1998 genes harbored potential compound heterozygous variants in the tested individuals and compound heterozygotes in 1066 genes occurred only in singular cases.</p

The length of the coding sequence and the mean number of rare alleles per gene.

<p>In an average healthy individual from the 5000 exomes project there is more than one rare heterozygous variant in <i>MUC16</i> that has an allele frequency below 0.01 in the reference population. In contrast, the coding sequence of <i>PIGO</i> is much shorter and rare heterozygous variants occur in less than 8 out of 1000 exomes.</p

Filtering results for compound heterozyotes in a case study.

<p>With the filter settings for genotype frequency <0.01, effect on protein level (functional filter: missense, nonsense, stop loss, splice site, insertions or deletions), and compound heterozygous yields six variants in three genes. <i>MUC16</i> and <i>NBPR10</i> are both genes from large gene families known for their high variability and detection artifacts due to pseudogenes. The heterozygotes in <i>PIGO</i> remain as the likeliest candidates. The <i>Show</i> icon at the right end of the line links to an expert curated annotation database that indicates that the mutation in <i>PIGO</i> is causing Hyperphosphatasia with mental retardation syndrome and has been published in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070151#pone.0070151-Krawitz1" target="_blank">[9]</a>. The gene view for <i>PIGO</i> lists all variant annotations for this gene and links to further knowledge bases. The length of the coding sequence of the longest transcript (max. CDS) and the mean number of rare heterozygous variant calls per exome (MRHC) are important parameters for the assessment of candidate genes.</p